Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016456.1 Corchorus olitorius cultivar O-4 contig16489, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 108959
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1855 original size:19 final size:19
Alignment explanation
Indices: 1835--1871 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1825 AATTAATTAT
1835 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
1853 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
1872 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:2086 original size:11 final size:11
Alignment explanation
Indices: 2070--2101 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
2060 TTGATATTTT
2070 ATACGGGTAGG
1 ATACGGGTAGG
2081 ATACGGGTAGG
1 ATACGGGTAGG
2092 ATACGGGTAG
1 ATACGGGTAG
2102 TGATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.44, T:0.19
Consensus pattern (11 bp):
ATACGGGTAGG
Found at i:3567 original size:30 final size:31
Alignment explanation
Indices: 3531--3589 Score: 111
Period size: 30 Copynumber: 1.9 Consensus size: 31
3521 GTTAATAAGC
3531 CATTAAAATTTGAGGGTATAAGA-GAAAAGT
1 CATTAAAATTTGAGGGTATAAGAGGAAAAGT
3561 CATTAAAATTTGAGGGTATAAGAGGAAAA
1 CATTAAAATTTGAGGGTATAAGAGGAAAA
3590 TCAAGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.25
Consensus pattern (31 bp):
CATTAAAATTTGAGGGTATAAGAGGAAAAGT
Found at i:4314 original size:50 final size:51
Alignment explanation
Indices: 4223--4322 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 51
4213 ATACCTTGCA
4223 TACTATGCAAAGTATATACTATGCATTTTCTCTTTTAATGTCAAGTTCCCAC
1 TACTATGCAAAGTATATAC-ATGCATTTTCTCTTTTAATGTCAAGTTCCCAC
* *
4275 TACTATGCAAGGTATATAC-TGCATTTTCTCTTTTCATGTCAAGTTCCC
1 TACTATGCAAAGTATATACATGCATTTTCTCTTTTAATGTCAAGTTCCC
4323 GATTCAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 28 0.61
52 18 0.39
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (51 bp):
TACTATGCAAAGTATATACATGCATTTTCTCTTTTAATGTCAAGTTCCCAC
Found at i:19741 original size:29 final size:30
Alignment explanation
Indices: 19698--19778 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 30
19688 TGCAATTTGC
* *
19698 TAAA-GTTTAGACTCAATTTGGTGT-TGTT
1 TAAAGGTTTAGCCTCAATTTGGTGTAAGTT
*
19726 TAAAGGTTTAGCCTCAAATT-GTGTAAGTT
1 TAAAGGTTTAGCCTCAATTTGGTGTAAGTT
19755 TGAAAAGGTTTAGACC-CAATTTGG
1 T--AAAGGTTTAG-CCTCAATTTGG
19779 ACATTAAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 8 0.19
29 17 0.40
31 15 0.35
32 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (30 bp):
TAAAGGTTTAGCCTCAATTTGGTGTAAGTT
Found at i:20566 original size:160 final size:160
Alignment explanation
Indices: 20327--20647 Score: 558
Period size: 161 Copynumber: 2.0 Consensus size: 160
20317 ATAAAAGATA
*
20327 ATAATTAAGGTTTGTCCCTTTGACTAAATTAAAAAGTTTTTGCTCAAAAAAGTTGAACCCAAAAC
1 ATAATTAAGGTTTGTCCCTCTGACTAAATTAAAAAGTTTTTGCTCAAAAAAGTTGAACCCAAAAC
*
20392 TAAATCATCTTCC-AATGTTGGGCACTAAATTAAACAATTAATTCCAGGTAAGAATAAAAGAAAG
66 TAAATCATCTTCCAAATGTTGGGCACCAAATTAAACAATTAA--CCAGG-AAGAATAAAAGAAAG
20456 AACGAAAAAGAAACATACGACATACTATAAAAG
128 AACGAAAAAGAAACATACGACATACTATAAAAG
*
20489 ATAA-TAAGGTTTGTCCCTCTGACTAAATTAAAAAG-TTTTGCTCAAAAAAGTTGAACCCAAAAT
1 ATAATTAAGGTTTGTCCCTCTGACTAAATTAAAAAGTTTTTGCTCAAAAAAGTTGAACCCAAAAC
*
20552 TAAATCATCTTCCAAATGTTGGGTACCAAATTAAACAATTAACCAGGAAGAATAAAAGAAAGAAC
66 TAAATCATCTTCCAAATGTTGGGCACCAAATTAAACAATTAACCAGGAAGAATAAAAGAAAGAAC
20617 GAAAAAGAAACATACGACATACTATAAAAG
131 GAAAAAGAAACATACGACATACTATAAAAG
20647 A
1 A
20648 CAAATTCTGT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
158 49 0.32
159 5 0.03
160 40 0.26
161 56 0.36
162 4 0.03
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (160 bp):
ATAATTAAGGTTTGTCCCTCTGACTAAATTAAAAAGTTTTTGCTCAAAAAAGTTGAACCCAAAAC
TAAATCATCTTCCAAATGTTGGGCACCAAATTAAACAATTAACCAGGAAGAATAAAAGAAAGAAC
GAAAAAGAAACATACGACATACTATAAAAG
Found at i:27548 original size:31 final size:31
Alignment explanation
Indices: 27508--27621 Score: 149
Period size: 31 Copynumber: 3.7 Consensus size: 31
27498 GCATACTATG
* *
27508 TGTATCAAAAAGCGACACGT-AGCACGCCACA
1 TGTACCAAAAAGTGACACGTGA-CACGCCACA
27539 TGTACCAAAAAGTGACACGTGACACGCCACA
1 TGTACCAAAAAGTGACACGTGACACGCCACA
* * * **
27570 TGTATCAAAAAGTGACACGTGTCATGCCATG
1 TGTACCAAAAAGTGACACGTGACACGCCACA
27601 TGTACCAAAAAGTGACACGTG
1 TGTACCAAAAAGTGACACGTG
27622 GCATACCTCG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 73 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.18
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACGTGACACGCCACA
Found at i:42314 original size:17 final size:17
Alignment explanation
Indices: 42292--42325 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42282 AACGGTTTCC
*
42292 AAGCAAGAAAATGAGCA
1 AAGCAACAAAATGAGCA
*
42309 AAGCAACAAAATTAGCA
1 AAGCAACAAAATGAGCA
42326 GCAGCACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.18, T:0.09
Consensus pattern (17 bp):
AAGCAACAAAATGAGCA
Found at i:44270 original size:31 final size:31
Alignment explanation
Indices: 44232--44292 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
44222 CCTGAGGCCA
* *
44232 AAACCCGA-ACCTGCATGACCCTAAATCCAGC
1 AAACCCGAGACCCGAATGA-CCTAAATCCAGC
*
44263 AAACCCGAGACCCGAATGACCTGAATCCAG
1 AAACCCGAGACCCGAATGACCTAAATCCAG
44293 ATGAGCCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.36, C:0.36, G:0.16, T:0.11
Consensus pattern (31 bp):
AAACCCGAGACCCGAATGACCTAAATCCAGC
Found at i:57608 original size:21 final size:21
Alignment explanation
Indices: 57581--57641 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
57571 ATGGGATTAC
57581 ACTGTACAGATGAGATTATGT
1 ACTGTACAGATGAGATTATGT
*
57602 ATTGTACAGATGAGATTATGT
1 ACTGTACAGATGAGATTATGT
*
57623 ACTATACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
57642 TAGAGCAGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:59980 original size:21 final size:21
Alignment explanation
Indices: 59954--59994 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
59944 GCTGCTCTAA
*
59954 TAATCTTATCTGTACAGTATC
1 TAATCTAATCTGTACAGTATC
59975 TAATCTAATCTGTACAGTAT
1 TAATCTAATCTGTACAGTAT
59995 AATCTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (21 bp):
TAATCTAATCTGTACAGTATC
Found at i:60080 original size:4 final size:4
Alignment explanation
Indices: 60071--60115 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
60061 ATCTTATTTC
60071 TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
60116 ATCTTAGGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 37 0.95
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:63130 original size:30 final size:30
Alignment explanation
Indices: 63075--63131 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
63065 TTTAATAGAC
* *
63075 TGAAATCTCAATTAAGGGCCTAATCTTTGT
1 TGAAATCTCAAATAAGGACCTAATCTTTGT
63105 TGAAATCTCAAATAAGGA-CTCAATCTT
1 TGAAATCTCAAATAAGGACCT-AATCTT
63132 CTAAAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (30 bp):
TGAAATCTCAAATAAGGACCTAATCTTTGT
Found at i:63695 original size:60 final size:61
Alignment explanation
Indices: 63564--63708 Score: 188
Period size: 60 Copynumber: 2.4 Consensus size: 61
63554 CAAACTGACG
*
63564 TCAGGCCCTTATTTGAGCATTTTCAATAAAACGTTAGACCCTTATTTGGCCAAATTAAAACA
1 TCAGGCCCTTATTTGAGCATTTTCAAT-AAACGTTAGACCCTTATTTGACCAAATTAAAACA
* * *
63626 -CTGGGCCCTTATTTGAGCATTTTCGAT-AACGTTAGACTCTTATTTGACCAAATTGAAAA-A
1 TC-AGGCCCTTATTTGAGCATTTTCAATAAACGTTAGACCCTTATTTGACCAAATT-AAAACA
* *
63686 TCAGACCCTTATTTGAACATTTT
1 TCAGGCCCTTATTTGAGCATTTT
63709 GACAAACATT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
60 44 0.60
61 6 0.08
62 23 0.32
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (61 bp):
TCAGGCCCTTATTTGAGCATTTTCAATAAACGTTAGACCCTTATTTGACCAAATTAAAACA
Found at i:63710 original size:29 final size:30
Alignment explanation
Indices: 63631--63710 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 30
63621 AAACACTGGG
* ** *
63631 CCCTTATTTGAGCATTTTCGATAACGTTAGA
1 CCCTTATTTGAACATTTT-GATAAAATCAGA
* * **
63662 CTCTTATTTGACCAAATTGA-AAAATCAGA
1 CCCTTATTTGAACATTTTGATAAAATCAGA
63691 CCCTTATTTGAACATTTTGA
1 CCCTTATTTGAACATTTTGA
63711 CAAACATTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
29 22 0.58
30 2 0.05
31 14 0.37
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (30 bp):
CCCTTATTTGAACATTTTGATAAAATCAGA
Found at i:66965 original size:16 final size:16
Alignment explanation
Indices: 66941--66971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66931 TAAAGGAGTA
*
66941 GGGTTCAACAAATAAC
1 GGGTGCAACAAATAAC
66957 GGGTGCAACAAATAA
1 GGGTGCAACAAATAA
66972 TATGCAACGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (16 bp):
GGGTGCAACAAATAAC
Found at i:71309 original size:15 final size:15
Alignment explanation
Indices: 71289--71318 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
71279 TATTAGTACC
71289 AAAAAAACAAAATAA
1 AAAAAAACAAAATAA
71304 AAAAAAACAAAATAA
1 AAAAAAACAAAATAA
71319 TACTAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAAAACAAAATAA
Found at i:71585 original size:31 final size:31
Alignment explanation
Indices: 71550--71719 Score: 115
Period size: 31 Copynumber: 5.6 Consensus size: 31
71540 TTGATGTCAT
* **
71550 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATATTAACAAACGTTAG
* *
71581 GCCCTTATTTG-GCCAAATT-A-AAA-GATTGG
1 GCCCTTATTTGAG-CATATTAACAAACG-TTAG
* * ** *
71610 GCTCTTATTTGAGCATCTTGGCAAATGTTAG
1 GCCCTTATTTGAGCATATTAACAAACGTTAG
* *
71641 GCCCTTATTTG-GCCAAATTAAAAAACCG---G
1 GCCCTTATTTGAG-CATATTAACAAA-CGTTAG
*
71670 GCCCTTATTTGAGCATTTTAACAAACGTTAG
1 GCCCTTATTTGAGCATATTAACAAACGTTAG
*
71701 ACCCTTATTTGAGCA-ATTA
1 GCCCTTATTTGAGCATATTA
71720 GCCAGCTAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.03
29 41 0.39
30 7 0.07
31 53 0.50
32 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GCCCTTATTTGAGCATATTAACAAACGTTAG
Found at i:71646 original size:60 final size:60
Alignment explanation
Indices: 71550--71711 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 60
71540 TTGATGTCAT
* **
71550 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCGG
* * *
71610 GCTCTTATTTGAGCATCTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAAACCGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCGG
** *
71670 GCCCTTATTTGAGCATTTTAACAAACGTTAGACCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
71712 AGCAATTAGC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCGG
Found at i:74683 original size:20 final size:20
Alignment explanation
Indices: 74658--74697 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
74648 AATTACAAAT
74658 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
74678 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
74698 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:82512 original size:2 final size:2
Alignment explanation
Indices: 82505--82577 Score: 52
Period size: 2 Copynumber: 38.5 Consensus size: 2
82495 CCGTTTAGTA
*
82505 AT AT AT AT A- AT -T AA AT AT AT AGT AT AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
82544 -T AG AT AT AT AT A- AT -T AT AT AT ACT AGT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT A
82578 ATTATTAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
1 7 0.12
2 44 0.77
3 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:90496 original size:18 final size:19
Alignment explanation
Indices: 90457--90496 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
90447 GTGCTCCCGT
90457 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
90478 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
90496 T
1 T
90497 TTTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:90729 original size:24 final size:24
Alignment explanation
Indices: 90702--90752 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
90692 TTTTTTATTT
*
90702 TTTATTCTTTTCTTCTCCGTTTTC
1 TTTATTCTCTTCTTCTCCGTTTTC
90726 TTTATTCTCTTCTTCTCCGTTTTC
1 TTTATTCTCTTCTTCTCCGTTTTC
90750 TTT
1 TTT
90753 TCCTGTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.04, C:0.25, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATTCTCTTCTTCTCCGTTTTC
Found at i:107283 original size:2 final size:2
Alignment explanation
Indices: 107276--107318 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
107266 TATTATAAGA
107276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107318 A
1 A
107319 GGCCGGCCGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.